Department Calendar of Events

External members are required to register to receive the link and passcode. Registration now closed!

James Collins, Massachusetts Institute of Technology

Host: Prof. Krishna Mahadevan

Synthetic biology is bringing together engineers, physicists and biologists to model, design and construct biological circuits out of proteins, genes and other bits of DNA, and to use these circuits to rewire and reprogram organisms.  These re-engineered organisms are going to change our lives in the coming years, leading to cheaper drugs, rapid diagnostic tests, and synthetic probiotics to treat infections and a range of complex diseases.  In this talk, we highlight recent efforts to create synthetic gene networks and programmable cells, and discuss a variety of synthetic biology applications in biotechnology and biomedicine.
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Professor James Collins is the Termeer Professor of Medical Engineering & Science and Professor of Biological Engineering at MIT, as well as a Member of the Harvard-MIT Health Sciences & Technology Faculty. He is also a Core Founding Faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard University, and an Institute Member of the Broad Institute of MIT and Harvard. He is one of the founders of the field of synthetic biology, and his research group is currently focused on using synthetic biology to create next-generation diagnostics and therapeutics. Professor Collins’ patented technologies have been licensed by over 25 biotech, pharma and medical devices companies, and he has co-founded a number of companies, including Synlogic, Senti Biosciences, Sherlock Biosciences and Cellarity, as well as Phare Bio, a non-profit focused on AI-driven antibiotic discovery. He has received numerous awards and honors, including a Rhodes Scholarship and a MacArthur “Genius” Award, and he is an elected member of all three national academies – the National Academy of Sciences, the National Academy of Engineering, and the National Academy of Medicine.

View the complete 2021-22 LLE schedule

Questions? Please contact Jennifer Hsu, Manager, External Relations  jennifer.hsu@utoronto.ca.

BioZone will be hosting Dr. Jens Kastenhofer, from our Dept. of Chemical Engineering & Applied Chemistry, on Thursday, October 28 from 3 pm – 4:30 pm.

Title: Extracellular production of recombinant proteins with E. coli

Abstract

Escherichia coli is among the most favored expression hosts for recombinant proteins. It grows fast on cheap media, is easily genetically manipulated and bears low risk of contamination. However, the product is usually located inside the cell, resulting in a complex and costly purification process. Extracellular production may alleviate this bottleneck but is difficult to achieve due to the nature of the E. coli cell envelope and missing secretory pathways.

Dr. Jens Kastenhofer will present various strategies on how to achieve extracellular production of recombinant proteins with E. coli and demonstrate its benefit for the downstream process, both economical and ecological. Furthermore, the talk will explore approaches to monitoring extracellular production processes with E. coli.

Speaker Bio

Jens Kastenhofer obtained his MSc degree from Wageningen University & Research (The Netherlands) and his PhD from TU Wien (Vienna, Austria). His doctoral research was concerned with novel techniques for recombinant protein production in E. coli. He was awarded with the Erwin-Schrödinger-Fellowship from the Austrian Science Fund (FWF) for a postdoc position at the Department of Chemical Engineering & Applied Chemistry, University of Toronto. In the lab of Prof. D. Grant Allen, he is working towards understanding the response of microalgae to rare earth elements.

To receive the Zoom link and passcode, please contact Sofia Bonilla (sofia.bonillatobar@mail.utoronto.ca) or Olan Raji (olan.raji@utoronto.ca)

Rachel O’Brien
Assistant Professor

Chemistry Department
College of William and Mary

Abstract:

Brown carbon (BrC) in aerosol particles and cloud droplets can contribute to climate warming by absorbing radiation in the visible region of the solar spectrum. Large uncertainties remain in our parameterization of this warming, in part due to a lack of knowledge about atmospheric lifetimes for the chromophores (the light absorbing structures in BrC molecules). An important removal pathway involves chemical transformations that fragment the chromophore, thus removing its ability to absorb visible light. However, the rates measured for this removal pathway in the laboratory are much shorter than what is observed in ambient measurements. There also can be different amounts of photo-resistant BrC, which is a fraction of the mixture that does not rapidly bleach and therefore affects the practical lifetime of the BrC. An important BrC source in the atmosphere is biomass burning and the overall photochemical decay rates for these emissions are important to quantify to improve our parameterizations for their radiative effects. In this talk, I will be combining results from work in our lab, along with a broader review of prior literature of photochemical bleaching, to evaluate gaps in our ability to predict the observed ambient removal rates using laboratory measurements. By probing complex mixtures from recent biomass burning experiments (e.g. FIREX samples), I will demonstrate that our current measured rates in the laboratory are overestimated and that a slower photolysis rate, as well as a potential gas-phase oxidation rate, should be included to better predict BrC lifetimes in the atmosphere.

For the Microsoft Teams Meeting details, please email natalieyl.leung@utoronto.ca.

External members are required to register to receive the link and passcode. Registration closed at 9am on Monday, November 15.

EDUCATION IN ENGINEERING LECTURE

Co-hosted with the Institute for Studies in Transdisciplinary Engineering Education & Practice (ISTEP)

Alice Pawley, Purdue

Host: Prof. Greg Evans

Social activism has increased, even during the COVID pandemic, around both systemic racism in North America and around the climate crisis internationally.  While both movements have roots decades old, we are not yet seeing a sea-change in engineering curricula around either, despite its necessity. I argue there are similarities between engineering education’s intransigence on social justice and equity issues and its lack of adequate response regarding the global climate crisis. Scholars in linguistics, education, sociology, and critical race studies, and journalists writing about the climate crisis, can help us see how both are related to a moral discussion rather than the techno-rational one that scientists, engineers, and science and engineering educators seem most equipped to have.  In this talk, I call for the development of a moral infrastructure to address both engineering education’s foundation in white supremacy, and its global obligation to halt the anthropogenic climate crisis.
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Alice Pawley (she, her) is a Professor in the School of Engineering Education and an affiliate faculty member in the Gender, Women’s and Sexuality Studies Program, the Purdue Climate Change Research Center, and the Division of Environmental and Ecological Engineering at Purdue University. Prof. Pawley’s goal through her work at Purdue is to help people, including the engineering education profession, develop a vision of engineering education as more inclusive, engaged, and socially just. She runs the Feminist Research in Engineering Education Group, whose diverse projects and group members are described at pawleyresearch.org. She has won numerous best paper awards in ASEE, and professional awards, including a PECASE award, ABIE Denice Denton award, the ASEE-LEES Sterling Olmsted award, and mentoring and leadership awards in her school. She helped found, fund, and grow the PEER Collaborative, a peer-mentoring community of academics primarily evaluated on doing engineering education research. She is president of Purdue’s chapter of the American Association of University Professors (2020-22).

View the complete 2021-22 LLE schedule

Questions? Please contact Jennifer Hsu, Manager, External Relations  jennifer.hsu@utoronto.ca.

BioZone will be hosting Tyler Irving, from our Faculty of Applied Science & Engineering on Thursday, November 25 from 3-4:30pm on Zoom.

Title: Science communication for fun and profit

Abstract
Science communication is a critical skill for anyone in STEM, but it can also be a career unto itself. Tyler will talk about his journey as a professional science writer/communicator and fold in some tips for anyone interested in either pursuing a similar path or simply improving their science communication practice.

Speaker Bio
Tyler Irving graduated with a MASc from U of T Engineering in 2010. He has since worked as a freelance science writer and communicator, as well as for a range of organizations, including the Canadian Chemical News, the Science Media Centre of Canada, and the University of Toronto. His work has won awards from Engineers Canada and from Science Writers and Communicators Canada.

To receive the Zoom link and passcode, please send an email to either Sofia Bonilla (sofia.bonillatobar@mail.utoronto.ca) or Olan Raji (olan.raji@utoronto.ca).

Life in a Tight Spot: How Bacteria Swim, Disperse, and Grow in Crowded Spaces
Speaker: Sujit Datta
Assistant Professor of Chemical and Biological Engineering, Princeton University

Join us:
Zoom link: https://utoronto.zoom.us/j/86762931790
Meeting ID: 867 6293 1790, Passcode: 759852

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Abstract
Bacterial motility and growth play central roles in agriculture, the environment, and medicine. While
bacterial behavior is typically studied in bulk liquid or on flat surfaces, many bacterial habitats—e.g.,
soils, sediments, and biological gels/tissues—are complex and crowded spaces. In this talk, I will
describe my group’s work using tools from soft matter engineering to address this gap in knowledge. In
particular, using studies of E. coli in transparent 3D porous media, we demonstrate how confinement in
a crowded medium fundamentally alters bacterial behavior. In particular, we show how the paradigm of
run-and-tumble motility is dramatically altered by pore-scale confinement, both for cells performing
undirected motion and those performing chemotaxis, directed motion in response to a chemical
stimulus. Our porous media also enable precisely structured multi-cellular communities to be 3D
printed. Using this capability, we show how spatial variations in the ability of cells to perform
chemotaxis enable populations to autonomously stabilize large-scale perturbations in their overall
morphology. Finally, we show how when the pores are small enough to prevent cells from swimming
through the pore space, expansion of a community via cellular growth and division gives rise to distinct,
highly-complex, large-scale community morphologies. Together, our work thus reveals new principles to
predict and control the behavior of bacteria, and active matter in general, in complex and crowded
environments

Biography
Sujit Datta is an Assistant Professor of Chemical and Biological Engineering at Princeton University. He
earned a BA in Mathematics and Physics and an MS in Physics in 2008 from the University of
Pennsylvania. He earned his PhD in Physics in 2013 from Harvard, where he studied fluid dynamics and
instabilities in porous media and colloidal microcapsules with David Weitz. His postdoctoral training was in Chemical Engineering at Caltech, where he studied the biophysics of the gut with Rustem Ismagilov.

He joined Princeton in 2017, where his lab studies the dynamics of soft and living materials in complex
environments. Prof. Datta is the recipient of the NSF CAREER Award, Pew Biomedical Scholar Award,
AIChE 35 Under 35 Award, ACS Unilever Award, APS Andreas Acrivos Award in Fluid Dynamics, and
multiple Commendations for Outstanding Teaching.

Research Webpage: http://dattalab.princeton.edu/

External members were required to register to receive the link and passcode. Registration closed at 9am on Monday, November 29th.

Gordana Vunjak-Novakovic, Columbia

Hosts: Profs Milica Radisic & Molly Shoichet

The classical paradigm of tissue engineering involves an integrated use of human stem cells, biomaterials (providing a specialized template for tissue formation) and bioreactors (providing environmental control, dynamic sequences of molecular and physical signals and insights into the structure and function of the forming tissues). This approach results in an increasingly successful representation of tissue development, regeneration and disease. Bioengineered human tissues are now being tailored to the patient and the condition being studied or treated. A reverse paradigm is emerging in recent years, with the emergence of “organs on a chip” platforms for modeling integrated human physiology, using micro-tissues derived from human iPS cells and linked by vascular perfusion. The common objectives are to recapitulate the cellular niches that can modulate cell behavior towards generating functional equivalents of native tissues. To illustrate the state of the art in the field and reflect on the current challenges and opportunities, this talk will discuss bioengineering of clinically relevant tissues and the use of “organs on a chip” platforms for patient-specific studies of human patho/physiology.
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Gordana Vunjak-Novakovic is University Professor, the highest academic rank at Columbia University and the first engineer at Columbia to receive this distinction. The focus of her lab is on engineering functional human tissues for use in regenerative medicine and patient-specific “organs-on-a-chip” for studies of human physiology in health and disease. She is well published and highly cited (h=132), has mentored over 150 trainees, and launched four biotech companies form her lab.

She is serving on the Council of the NIBIB, the HHMI Scientific Review Board, and on numerous editorial and scientific advisory boards. She was inducted into the Women in Technology International Hall of Fame, received the Clemson Award of the Biomaterials Society, Pritzker Award of the Biomedical Engineering Society, Shu Chien Award of the AIChE, Pierre Galletti award of the AIMBE, and was elected Fellow of several professional societies. She was decorated by the Order of Karadjordje Star – Serbia’s highest honor, and elected to the Academia Europaea, Serbian Academy of Arts and Sciences, the National Academy of Engineering, National Academy of Medicine, National Academy of Inventors, the American Academy of Arts and Sciences and the International Academy for Medical and Biological Engineering.

View the complete 2021-22 LLE schedule

Questions? Please contact Delicia Ansalem, Communications Officer & External Relations Liaison delicia.ansalem@utoronto.ca

Upcoming SOCAAR Seminar:

Wednesday, December 1, 2021
3:00 – 4:00PM Join on
MS Teams (see below)

Elisabeth Galarneau, Ph.D.
Research Scientist

Air Quality Research Division
Environment and Climate Change Canada

Polycyclic aromatic compounds and other air toxics: toward understanding the whole air pollutant mixture.

Air quality issues have traditionally been divided between common air pollutants like ozone and contaminants such as polycyclic aromatic compounds (PACs). Research has tended to be conducted by experts who are largely separated, who publish in different journals and attend different conferences. Environmental management has been distinct as well, with national programs and international agreements designed and implemented by different groups for ‘smog’ and ‘contaminants’. More recently, air quality research and management have begun to acknowledge that exposure and effects are affected by the simultaneous presence of multiple pollutants.  The whole air pollutant mixture has not yet been well-characterized at any location. Canadian efforts associated with PACs, air toxics and the urban air pollution mixture will be discussed to demonstrate how we can begin to better understand ambient air and its overall impacts on human health and the environment.

For more information, see the full abstract: https://t.co/Vb2MA6hxTz?amp
If you have any questions, please contact socaar@utoronto.ca

Redesigning Drug Design by Dr. John Chodera
Wednesday, December 8th @ 10:00AM
Zoom Link: https://utoronto.zoom.us/j/87130346324
Passcode: 398523
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As machine learning and physical modeling technologies are reaching maturity, a new era of technological innovation in computer-driven drug discovery is dawning. In this talk, we highlight an exciting new generation of tools that blend machine learning with physical modeling to accelerate structure-enabled drug discovery programs, with the goal of ultimately enabling fully autonomous drug discovery. We also highlight the role these tools have played in the COVID Moonshot, an open science global collaborative effort to discover a novel patent-free oral SARSCoV-2 antiviral with the goal of rapid, global, and equitable access.

John Chodera’s research focuses on reimagining the way we develop small molecule drugs and pair therapeutics with individual patient tumors by bringing physical modeling and structure-informed machine learning into the cancer genomics era. By combining novel algorithmic advances to achieve orders-of-magnitude efficiency gains with powerful but inexpensive GPU hardware, machine learning, and distributed computing technologies, the Chodera lab is developing next-generation approaches and open source software for predicting small molecule binding affinities, designing small molecules with desired properties, predicting drug sensitivity or resistance of clinical mutations, and understanding the detailed structural mechanisms underlying oncogenic mutations. The Chodera lab co-develops the OpenMM GPU-powered molecular simulation framework, which powers numerous biomolecular modeling and simulation applications using physical modeling and machine learning. As a core member of the Folding@home Consortium, the lab harnesses the largest computing platform in the world—the first to reach an exaFLOP/s—pooling the efforts of a million volunteers around the world to study functional implications of mutations and new opportunities for therapeutic design against cancer targets and global pandemics. Dr. Chodera co-founded the Open Force Field Initiative, a scientific collaboration funded by the NIH and an industry consortium consisting of dozens of scientists working to develop modern open source infrastructure for building and applying high-quality biomolecular force fields. Dr. Chodera is a co-founder of the COVID Moonshot, a radical open science patent-free drug discovery effort aiming to develop an inexpensive small molecule therapy effective against COVID-19 and future coronavirus. Using automated biophysical measurements, the Chodera laboratory collects new experimental data targeted to advance the quantitative accuracy of our methodologies, and gather new insight into drug susceptibility and resistance in kinases and other cancer targets. Their work makes extensive use of scalable Bayesian statistical inference, machine learning via probabilistic programming, and information theoretic principles for designing experiments and quantifying error. Dr. Chodera is passionate about open science, disseminating scientific best practices, and maximizing research reproducibility